Package picard.sam

Class AddCommentsToBam


  • @DocumentedFeature
    public class AddCommentsToBam
    extends CommandLineProgram
    A tool to add comments to a BAM file header. Effectively copies the BAM file except for the addition of the @CO records in the header. This tool does not support SAM files. A block copying method is used to ensure efficient transfer to the output file.
    • Field Detail

      • INPUT

        @Argument(shortName="I",
                  doc="Input BAM file to add a comment to the header")
        public File INPUT
      • OUTPUT

        @Argument(shortName="O",
                  doc="Output BAM file to write results")
        public File OUTPUT
      • COMMENT

        @Argument(shortName="C",
                  doc="Comments to add to the BAM file")
        public List<String> COMMENT
    • Constructor Detail

      • AddCommentsToBam

        public AddCommentsToBam()
    • Method Detail

      • doWork

        protected int doWork()
        Description copied from class: CommandLineProgram
        Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.
        Specified by:
        doWork in class CommandLineProgram
        Returns:
        program exit status.